GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gtsD in Pseudomonas stutzeri RCH2

Align ABC transporter for D-Galactose and D-Glucose, ATPase component (characterized)
to candidate GFF1860 Psest_1899 ABC-type sugar transport systems, ATPase components

Query= reanno::pseudo13_GW456_L13:PfGW456L13_1897
         (386 letters)



>FitnessBrowser__psRCH2:GFF1860
          Length = 390

 Score =  557 bits (1436), Expect = e-163
 Identities = 287/368 (77%), Positives = 317/368 (86%), Gaps = 2/368 (0%)

Query: 1   MATLELRNVNKTYGPGLPDTLKNIELKIDDGEFLILVGPSGCGKSTLMNCIAGLETISGG 60
           MA+LELRNV K+YG     TLK+I LKID GEFLILVGPSGCGKSTLMNCIAGLE I+GG
Sbjct: 1   MASLELRNVQKSYGNSQIATLKDIALKIDAGEFLILVGPSGCGKSTLMNCIAGLENITGG 60

Query: 61  AILVDDADISGMSPKDRDIAMVFQSYALYPTMSVRDNIAFGLKIRKMPTAEIDEEVARVS 120
            ILVD  DIS  SPKDRDIAMVFQSYALYPTMSVRDNIAFGLK+RK+P A+I+EEVARV+
Sbjct: 61  EILVDGEDISQASPKDRDIAMVFQSYALYPTMSVRDNIAFGLKMRKVPAAKIEEEVARVA 120

Query: 121 KLLQIEHLLSRKPGQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEMKL 180
           KLLQIE LL RKP QLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTE+KL
Sbjct: 121 KLLQIEPLLERKPSQLSGGQQQRVAMGRALARRPKIYLFDEPLSNLDAKLRVEMRTEIKL 180

Query: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGIIQQFGTPKDIYNNPANLFVASFIGSPP 240
           MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDG+IQQFGTP +IYNNPANLFVASFIGSPP
Sbjct: 181 MHQRLKTTTVYVTHDQIEAMTLGDKVAVMKDGVIQQFGTPHEIYNNPANLFVASFIGSPP 240

Query: 241 MNFIPLRLQRKDGRLLALLDSGQARCELPLGM-QDAGLEDREVILGIRPEQIILANGEAN 299
           MNF+PLR++++DGR + +L+S Q  CELPL +  D GL DRE+ILGIRPEQI LA   + 
Sbjct: 241 MNFVPLRIRQRDGRWVGVLNSEQGSCELPLPITSDDGLRDRELILGIRPEQIGLAPAGSA 300

Query: 300 GLPTIRAEVQVTEPTGPDTLVFVNLNDTKVCCRLAPDVAPAVGETLTLQFDPAKVLLFDA 359
              ++  +++V EPTGPDTLV   LN  K CCRLAPD AP VGETL LQFDP + LLFDA
Sbjct: 301 DF-SLAVDIEVVEPTGPDTLVVFTLNQVKACCRLAPDQAPRVGETLNLQFDPRRALLFDA 359

Query: 360 KTGERLGV 367
           +TGERLGV
Sbjct: 360 QTGERLGV 367


Lambda     K      H
   0.319    0.138    0.393 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 519
Number of extensions: 11
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 386
Length of database: 390
Length adjustment: 30
Effective length of query: 356
Effective length of database: 360
Effective search space:   128160
Effective search space used:   128160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 50 (23.9 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

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About GapMind

Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.

A candidate for a step is "high confidence" if either:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

Otherwise, a candidate is "medium confidence" if either:

Other blast hits with at least 50% coverage are "low confidence."

Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:

GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).

For more information, see:

If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know

by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory